Starting phenix.real_space_refine on Sun Mar 10 20:53:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1v_22630/03_2024/7k1v_22630.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1v_22630/03_2024/7k1v_22630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1v_22630/03_2024/7k1v_22630.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1v_22630/03_2024/7k1v_22630.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1v_22630/03_2024/7k1v_22630.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1v_22630/03_2024/7k1v_22630.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 9 5.16 5 C 3138 2.51 5 N 888 2.21 5 O 936 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 37": "OE1" <-> "OE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ASP 166": "OD1" <-> "OD2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A ASP 362": "OD1" <-> "OD2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 519": "OD1" <-> "OD2" Residue "A ASP 520": "OD1" <-> "OD2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 560": "OE1" <-> "OE2" Residue "A TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 588": "OD1" <-> "OD2" Residue "A PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 648": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4971 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 4971 Classifications: {'peptide': 626} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 599} Chain breaks: 3 Time building chain proxies: 3.26, per 1000 atoms: 0.66 Number of scatterers: 4971 At special positions: 0 Unit cell: (90.355, 76.536, 91.418, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 9 16.00 O 936 8.00 N 888 7.00 C 3138 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 878.1 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 3 sheets defined 60.1% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 19 through 28 removed outlier: 8.375A pdb=" N PHE A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLY A 26 " --> pdb=" O ASP A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 36 removed outlier: 3.759A pdb=" N LEU A 33 " --> pdb=" O ASN A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 69 removed outlier: 3.678A pdb=" N GLN A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASP A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 removed outlier: 3.745A pdb=" N ASP A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 removed outlier: 3.606A pdb=" N ARG A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 111 removed outlier: 3.587A pdb=" N LEU A 101 " --> pdb=" O GLY A 97 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 127 removed outlier: 3.895A pdb=" N THR A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 166 removed outlier: 4.448A pdb=" N ARG A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 193 through 210 removed outlier: 4.040A pdb=" N VAL A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU A 206 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 221 removed outlier: 3.667A pdb=" N ARG A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 267 through 278 Processing helix chain 'A' and resid 279 through 295 removed outlier: 3.988A pdb=" N CYS A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TRP A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 303 through 312 removed outlier: 3.706A pdb=" N ASP A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 328 through 336 removed outlier: 4.122A pdb=" N VAL A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASN A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 352 through 372 removed outlier: 4.081A pdb=" N ARG A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASP A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASN A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 372 " --> pdb=" O TYR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 removed outlier: 4.164A pdb=" N ARG A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 437 removed outlier: 3.719A pdb=" N VAL A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLU A 431 " --> pdb=" O ASN A 427 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 432 " --> pdb=" O HIS A 428 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 433 " --> pdb=" O ASP A 429 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 434 " --> pdb=" O ARG A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 499 removed outlier: 3.787A pdb=" N ASN A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE A 487 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 517 through 528 removed outlier: 3.662A pdb=" N ARG A 521 " --> pdb=" O THR A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 535 through 537 No H-bonds generated for 'chain 'A' and resid 535 through 537' Processing helix chain 'A' and resid 558 through 572 removed outlier: 4.592A pdb=" N GLY A 563 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP A 564 " --> pdb=" O GLU A 560 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE A 570 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 591 through 602 removed outlier: 3.529A pdb=" N TRP A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN A 602 " --> pdb=" O PHE A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 616 Processing helix chain 'A' and resid 617 through 620 removed outlier: 3.866A pdb=" N ASP A 620 " --> pdb=" O LEU A 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 617 through 620' Processing helix chain 'A' and resid 624 through 629 removed outlier: 3.823A pdb=" N ARG A 628 " --> pdb=" O PRO A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.707A pdb=" N ARG A 634 " --> pdb=" O GLY A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA3, first strand: chain 'A' and resid 454 through 455 removed outlier: 3.757A pdb=" N TYR A 454 " --> pdb=" O VAL A 463 " (cutoff:3.500A) 183 hydrogen bonds defined for protein. 531 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1509 1.34 - 1.45: 969 1.45 - 1.57: 2598 1.57 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 5092 Sorted by residual: bond pdb=" N VAL A 397 " pdb=" CA VAL A 397 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.11e-02 8.12e+03 1.27e+01 bond pdb=" N VAL A 543 " pdb=" CA VAL A 543 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.99e+00 bond pdb=" N ARG A 146 " pdb=" CA ARG A 146 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.90e+00 bond pdb=" N ILE A 156 " pdb=" CA ILE A 156 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.10e-02 8.26e+03 8.69e+00 bond pdb=" N TYR A 538 " pdb=" CA TYR A 538 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.18e-02 7.18e+03 8.23e+00 ... (remaining 5087 not shown) Histogram of bond angle deviations from ideal: 100.59 - 107.36: 207 107.36 - 114.14: 2610 114.14 - 120.91: 2467 120.91 - 127.69: 1571 127.69 - 134.47: 73 Bond angle restraints: 6928 Sorted by residual: angle pdb=" N ARG A 126 " pdb=" CA ARG A 126 " pdb=" C ARG A 126 " ideal model delta sigma weight residual 111.36 104.92 6.44 1.09e+00 8.42e-01 3.49e+01 angle pdb=" CA GLY A 398 " pdb=" C GLY A 398 " pdb=" O GLY A 398 " ideal model delta sigma weight residual 122.24 117.27 4.97 8.70e-01 1.32e+00 3.27e+01 angle pdb=" C GLU A 443 " pdb=" N TRP A 444 " pdb=" CA TRP A 444 " ideal model delta sigma weight residual 122.85 115.45 7.40 1.39e+00 5.18e-01 2.83e+01 angle pdb=" N ARG A 385 " pdb=" CA ARG A 385 " pdb=" C ARG A 385 " ideal model delta sigma weight residual 111.36 106.11 5.25 1.09e+00 8.42e-01 2.32e+01 angle pdb=" N ARG A 527 " pdb=" CA ARG A 527 " pdb=" C ARG A 527 " ideal model delta sigma weight residual 111.40 106.09 5.31 1.22e+00 6.72e-01 1.90e+01 ... (remaining 6923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 2585 17.19 - 34.39: 320 34.39 - 51.58: 63 51.58 - 68.77: 13 68.77 - 85.97: 4 Dihedral angle restraints: 2985 sinusoidal: 1180 harmonic: 1805 Sorted by residual: dihedral pdb=" CA VAL A 28 " pdb=" C VAL A 28 " pdb=" N ASN A 29 " pdb=" CA ASN A 29 " ideal model delta harmonic sigma weight residual -180.00 -151.64 -28.36 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA LEU A 390 " pdb=" C LEU A 390 " pdb=" N ASN A 391 " pdb=" CA ASN A 391 " ideal model delta harmonic sigma weight residual 180.00 152.19 27.81 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ALA A 127 " pdb=" C ALA A 127 " pdb=" N GLY A 128 " pdb=" CA GLY A 128 " ideal model delta harmonic sigma weight residual 180.00 152.19 27.81 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 2982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 542 0.056 - 0.111: 157 0.111 - 0.167: 30 0.167 - 0.222: 5 0.222 - 0.278: 2 Chirality restraints: 736 Sorted by residual: chirality pdb=" CA ARG A 126 " pdb=" N ARG A 126 " pdb=" C ARG A 126 " pdb=" CB ARG A 126 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA LYS A 396 " pdb=" N LYS A 396 " pdb=" C LYS A 396 " pdb=" CB LYS A 396 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA LEU A 158 " pdb=" N LEU A 158 " pdb=" C LEU A 158 " pdb=" CB LEU A 158 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 733 not shown) Planarity restraints: 920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 145 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.75e+00 pdb=" C THR A 145 " -0.051 2.00e-02 2.50e+03 pdb=" O THR A 145 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG A 146 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 321 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C LEU A 321 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU A 321 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG A 322 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 620 " -0.037 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO A 621 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 621 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 621 " -0.031 5.00e-02 4.00e+02 ... (remaining 917 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 204 2.71 - 3.26: 5699 3.26 - 3.80: 8722 3.80 - 4.35: 11468 4.35 - 4.90: 16634 Nonbonded interactions: 42727 Sorted by model distance: nonbonded pdb=" O ASP A 140 " pdb=" OD1 ASP A 140 " model vdw 2.159 3.040 nonbonded pdb=" O ARG A 327 " pdb=" OG SER A 330 " model vdw 2.208 2.440 nonbonded pdb=" O GLY A 566 " pdb=" OG SER A 569 " model vdw 2.235 2.440 nonbonded pdb=" NE2 GLN A 365 " pdb=" O LEU A 390 " model vdw 2.237 2.520 nonbonded pdb=" OE1 GLN A 65 " pdb=" NH1 ARG A 347 " model vdw 2.259 2.520 ... (remaining 42722 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.510 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.240 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 5092 Z= 0.488 Angle : 1.116 9.430 6928 Z= 0.666 Chirality : 0.055 0.278 736 Planarity : 0.006 0.055 920 Dihedral : 15.771 85.967 1825 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 0.40 % Allowed : 6.39 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.29), residues: 618 helix: -3.36 (0.23), residues: 209 sheet: -5.41 (0.56), residues: 10 loop : -2.32 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 32 HIS 0.008 0.002 HIS A 536 PHE 0.027 0.003 PHE A 652 TYR 0.032 0.003 TYR A 484 ARG 0.008 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 PHE cc_start: 0.8279 (m-80) cc_final: 0.7755 (m-10) REVERT: A 266 ASP cc_start: 0.8907 (m-30) cc_final: 0.8125 (t0) REVERT: A 293 ARG cc_start: 0.8677 (ttt-90) cc_final: 0.8169 (tpp80) REVERT: A 366 GLU cc_start: 0.8541 (tp30) cc_final: 0.7928 (tm-30) REVERT: A 397 VAL cc_start: 0.8160 (OUTLIER) cc_final: 0.7924 (p) REVERT: A 431 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8107 (pp20) REVERT: A 462 ILE cc_start: 0.7452 (pt) cc_final: 0.7099 (pt) REVERT: A 480 GLU cc_start: 0.9158 (tm-30) cc_final: 0.8852 (tm-30) REVERT: A 484 TYR cc_start: 0.8344 (t80) cc_final: 0.7779 (t80) REVERT: A 543 VAL cc_start: 0.1595 (OUTLIER) cc_final: 0.1339 (m) outliers start: 2 outliers final: 0 residues processed: 113 average time/residue: 0.2818 time to fit residues: 37.7211 Evaluate side-chains 80 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 227 ASN A 319 GLN A 346 GLN ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5092 Z= 0.188 Angle : 0.665 7.156 6928 Z= 0.353 Chirality : 0.043 0.139 736 Planarity : 0.005 0.047 920 Dihedral : 6.762 23.851 696 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.30), residues: 618 helix: -2.56 (0.22), residues: 315 sheet: -3.55 (1.69), residues: 10 loop : -2.15 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 286 HIS 0.007 0.001 HIS A 493 PHE 0.016 0.002 PHE A 652 TYR 0.010 0.001 TYR A 454 ARG 0.017 0.001 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 PHE cc_start: 0.8385 (m-80) cc_final: 0.8028 (m-80) REVERT: A 266 ASP cc_start: 0.8934 (m-30) cc_final: 0.8238 (t0) REVERT: A 462 ILE cc_start: 0.7341 (pt) cc_final: 0.7032 (pt) REVERT: A 534 GLN cc_start: 0.8093 (mt0) cc_final: 0.7854 (mp10) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2368 time to fit residues: 25.8883 Evaluate side-chains 66 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 HIS A 582 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5092 Z= 0.190 Angle : 0.599 10.252 6928 Z= 0.316 Chirality : 0.041 0.153 736 Planarity : 0.005 0.043 920 Dihedral : 6.020 23.474 696 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.20 % Allowed : 4.59 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.32), residues: 618 helix: -1.91 (0.25), residues: 323 sheet: -2.91 (1.75), residues: 10 loop : -1.66 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 286 HIS 0.005 0.001 HIS A 213 PHE 0.015 0.002 PHE A 308 TYR 0.012 0.002 TYR A 484 ARG 0.003 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.9216 (mpt180) cc_final: 0.8831 (mmt-90) REVERT: A 53 ASP cc_start: 0.9368 (t70) cc_final: 0.9152 (t0) REVERT: A 231 PHE cc_start: 0.8373 (m-80) cc_final: 0.8012 (m-10) REVERT: A 257 MET cc_start: -0.1885 (mtt) cc_final: -0.3016 (mtt) REVERT: A 266 ASP cc_start: 0.8875 (m-30) cc_final: 0.8224 (t0) REVERT: A 462 ILE cc_start: 0.7417 (pt) cc_final: 0.7178 (pt) REVERT: A 534 GLN cc_start: 0.8158 (mt0) cc_final: 0.7629 (tm-30) REVERT: A 582 ASN cc_start: 0.9354 (m-40) cc_final: 0.8868 (t0) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.2156 time to fit residues: 22.3982 Evaluate side-chains 61 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 HIS ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 5092 Z= 0.324 Angle : 0.725 10.629 6928 Z= 0.390 Chirality : 0.045 0.157 736 Planarity : 0.006 0.045 920 Dihedral : 6.543 25.308 696 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 35.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 0.40 % Allowed : 4.19 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.32), residues: 618 helix: -1.91 (0.24), residues: 331 sheet: -2.20 (1.83), residues: 10 loop : -1.74 (0.39), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 286 HIS 0.008 0.002 HIS A 428 PHE 0.017 0.003 PHE A 652 TYR 0.022 0.003 TYR A 575 ARG 0.006 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.9377 (mpt180) cc_final: 0.9071 (mmt-90) REVERT: A 231 PHE cc_start: 0.8338 (m-80) cc_final: 0.7927 (m-10) REVERT: A 257 MET cc_start: -0.0951 (mtt) cc_final: -0.2298 (mtt) REVERT: A 266 ASP cc_start: 0.8982 (m-30) cc_final: 0.8293 (t0) REVERT: A 462 ILE cc_start: 0.7806 (pt) cc_final: 0.7545 (pt) REVERT: A 534 GLN cc_start: 0.8302 (mt0) cc_final: 0.8026 (mp10) REVERT: A 602 GLN cc_start: 0.9384 (mp10) cc_final: 0.9084 (mp10) REVERT: A 604 TRP cc_start: 0.5524 (m100) cc_final: 0.5289 (m100) outliers start: 2 outliers final: 1 residues processed: 84 average time/residue: 0.2175 time to fit residues: 22.6510 Evaluate side-chains 67 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 0.0980 chunk 51 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5092 Z= 0.173 Angle : 0.605 11.076 6928 Z= 0.315 Chirality : 0.041 0.133 736 Planarity : 0.005 0.043 920 Dihedral : 5.890 23.423 696 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.32), residues: 618 helix: -1.43 (0.26), residues: 328 sheet: -2.06 (1.81), residues: 10 loop : -1.62 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 286 HIS 0.004 0.001 HIS A 213 PHE 0.016 0.002 PHE A 151 TYR 0.014 0.001 TYR A 164 ARG 0.002 0.000 ARG A 616 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.9227 (mpt180) cc_final: 0.8816 (mmt-90) REVERT: A 183 MET cc_start: 0.4914 (tpp) cc_final: 0.4558 (tpt) REVERT: A 231 PHE cc_start: 0.8042 (m-80) cc_final: 0.7678 (m-10) REVERT: A 257 MET cc_start: -0.1933 (mtt) cc_final: -0.2758 (mtt) REVERT: A 266 ASP cc_start: 0.8856 (m-30) cc_final: 0.8358 (t0) REVERT: A 462 ILE cc_start: 0.7371 (pt) cc_final: 0.7149 (pt) REVERT: A 582 ASN cc_start: 0.9339 (m-40) cc_final: 0.8572 (t0) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2061 time to fit residues: 20.4751 Evaluate side-chains 63 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 34 optimal weight: 50.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.5420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5092 Z= 0.166 Angle : 0.604 9.773 6928 Z= 0.311 Chirality : 0.042 0.192 736 Planarity : 0.004 0.042 920 Dihedral : 5.569 21.672 696 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.33), residues: 618 helix: -1.21 (0.26), residues: 329 sheet: -1.71 (1.85), residues: 10 loop : -1.38 (0.40), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 286 HIS 0.004 0.001 HIS A 213 PHE 0.014 0.002 PHE A 308 TYR 0.010 0.001 TYR A 164 ARG 0.003 0.000 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.9210 (mpt180) cc_final: 0.8860 (mpt180) REVERT: A 90 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7096 (mm-30) REVERT: A 183 MET cc_start: 0.4963 (tpp) cc_final: 0.4584 (tpt) REVERT: A 231 PHE cc_start: 0.8057 (m-80) cc_final: 0.7651 (m-10) REVERT: A 257 MET cc_start: -0.2147 (mtt) cc_final: -0.2852 (mtt) REVERT: A 266 ASP cc_start: 0.8904 (m-30) cc_final: 0.8289 (t0) REVERT: A 378 MET cc_start: 0.2463 (tpp) cc_final: 0.2242 (ttt) REVERT: A 582 ASN cc_start: 0.9318 (m-40) cc_final: 0.8670 (t0) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2062 time to fit residues: 19.5277 Evaluate side-chains 63 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 ASN ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 5092 Z= 0.366 Angle : 0.759 10.588 6928 Z= 0.405 Chirality : 0.047 0.222 736 Planarity : 0.006 0.046 920 Dihedral : 6.323 24.698 696 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 38.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.33), residues: 618 helix: -1.46 (0.25), residues: 335 sheet: -1.10 (2.05), residues: 10 loop : -1.48 (0.41), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 286 HIS 0.011 0.003 HIS A 213 PHE 0.020 0.003 PHE A 151 TYR 0.020 0.003 TYR A 163 ARG 0.013 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.9347 (mpt180) cc_final: 0.9000 (mmt-90) REVERT: A 231 PHE cc_start: 0.8256 (m-80) cc_final: 0.7869 (m-10) REVERT: A 257 MET cc_start: -0.1173 (mtt) cc_final: -0.2209 (mtt) REVERT: A 266 ASP cc_start: 0.9186 (m-30) cc_final: 0.8485 (t70) REVERT: A 462 ILE cc_start: 0.7755 (pt) cc_final: 0.7469 (pt) REVERT: A 470 GLN cc_start: 0.9533 (tt0) cc_final: 0.9251 (tt0) REVERT: A 582 ASN cc_start: 0.9383 (m-40) cc_final: 0.8497 (t0) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2244 time to fit residues: 22.5447 Evaluate side-chains 64 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5092 Z= 0.181 Angle : 0.637 8.340 6928 Z= 0.334 Chirality : 0.044 0.216 736 Planarity : 0.005 0.041 920 Dihedral : 5.757 22.020 696 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.34), residues: 618 helix: -0.97 (0.28), residues: 333 sheet: -1.32 (2.03), residues: 10 loop : -1.43 (0.40), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 214 HIS 0.006 0.001 HIS A 213 PHE 0.015 0.002 PHE A 151 TYR 0.012 0.001 TYR A 164 ARG 0.007 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.8527 (t-90) cc_final: 0.8045 (t-90) REVERT: A 31 ARG cc_start: 0.9082 (mpt180) cc_final: 0.8711 (mmt-90) REVERT: A 231 PHE cc_start: 0.8073 (m-80) cc_final: 0.7712 (m-10) REVERT: A 257 MET cc_start: -0.2282 (mtt) cc_final: -0.2947 (mtt) REVERT: A 266 ASP cc_start: 0.8962 (m-30) cc_final: 0.8549 (t0) REVERT: A 462 ILE cc_start: 0.7240 (pt) cc_final: 0.6988 (pt) REVERT: A 582 ASN cc_start: 0.9378 (m-40) cc_final: 0.8579 (t0) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2056 time to fit residues: 19.1793 Evaluate side-chains 60 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 0.0030 chunk 52 optimal weight: 0.0980 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.6284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5092 Z= 0.168 Angle : 0.622 11.916 6928 Z= 0.315 Chirality : 0.043 0.209 736 Planarity : 0.005 0.042 920 Dihedral : 5.391 24.712 696 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.20 % Allowed : 1.00 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.34), residues: 618 helix: -0.76 (0.28), residues: 333 sheet: -1.49 (2.00), residues: 10 loop : -1.35 (0.40), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 214 HIS 0.005 0.001 HIS A 213 PHE 0.014 0.001 PHE A 308 TYR 0.008 0.001 TYR A 399 ARG 0.005 0.001 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 PHE cc_start: 0.8079 (m-80) cc_final: 0.7710 (m-10) REVERT: A 257 MET cc_start: -0.2100 (mtt) cc_final: -0.2474 (mtt) REVERT: A 263 ARG cc_start: 0.8508 (mtp180) cc_final: 0.7725 (tpt170) REVERT: A 266 ASP cc_start: 0.8951 (m-30) cc_final: 0.8568 (t0) REVERT: A 446 MET cc_start: 0.7050 (ppp) cc_final: 0.6831 (ppp) REVERT: A 462 ILE cc_start: 0.7183 (pt) cc_final: 0.6963 (pt) outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.2234 time to fit residues: 20.3649 Evaluate side-chains 60 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.2980 chunk 56 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 37 optimal weight: 0.4980 chunk 30 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.6519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5092 Z= 0.168 Angle : 0.624 11.475 6928 Z= 0.317 Chirality : 0.044 0.192 736 Planarity : 0.004 0.042 920 Dihedral : 5.307 25.108 696 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.34), residues: 618 helix: -0.75 (0.28), residues: 336 sheet: -1.82 (1.79), residues: 10 loop : -1.39 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 214 HIS 0.005 0.001 HIS A 213 PHE 0.013 0.001 PHE A 308 TYR 0.015 0.001 TYR A 368 ARG 0.009 0.001 ARG A 413 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 PHE cc_start: 0.8068 (m-80) cc_final: 0.7712 (m-10) REVERT: A 257 MET cc_start: -0.1665 (mtt) cc_final: -0.2047 (mtt) REVERT: A 266 ASP cc_start: 0.8918 (m-30) cc_final: 0.8570 (t0) REVERT: A 446 MET cc_start: 0.7179 (ppp) cc_final: 0.6933 (ppp) REVERT: A 447 THR cc_start: 0.8652 (m) cc_final: 0.8430 (m) REVERT: A 462 ILE cc_start: 0.7144 (pt) cc_final: 0.6882 (pt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2502 time to fit residues: 24.4126 Evaluate side-chains 61 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.143730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.115349 restraints weight = 20360.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 14)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.115911 restraints weight = 19334.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.116905 restraints weight = 18598.884| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.6598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5092 Z= 0.262 Angle : 0.674 10.860 6928 Z= 0.350 Chirality : 0.045 0.187 736 Planarity : 0.005 0.043 920 Dihedral : 5.602 24.923 696 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 31.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 0.20 % Allowed : 0.40 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.34), residues: 618 helix: -0.80 (0.28), residues: 323 sheet: -1.60 (1.93), residues: 10 loop : -1.24 (0.40), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 286 HIS 0.007 0.002 HIS A 428 PHE 0.016 0.002 PHE A 308 TYR 0.014 0.002 TYR A 164 ARG 0.011 0.001 ARG A 413 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1339.71 seconds wall clock time: 25 minutes 10.85 seconds (1510.85 seconds total)